*NCBI Gene # or RefSeq#: *Protein ID (NP or XP #) or Wolbachia#: TGME49_242600-t26_1 *Organism (including strain): Toxoplasma gondii Etiologic Risk Group (see link below): */Disease Information (sort of like the Intro to your Mini Research Write up): Toxoplasma gondii is a single-celled parasite that causes the disease known as toxoplasmosis. In the United States alone, more than 60 million people are infected with the parasite, however very few express symptoms because a healthy person's immune system usually keeps the parasite from causing illness. Pregnant women and individuals with compromised immune systems are the most at risk for contracting taxoplasmosis. The most common way of getting a taxoplasma infection is through the consumption or handling (and not washing hands properly) of undercooked meat. Link to TDR Targets page (if present): http://www.tdrtargets.org/targets/view?gene_id=258054 Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.):http://toxodb.org/toxo/app/record/gene/TGME49_042600 Essentiality of this protein: TGME49_042600 has essentiality data Gene/Ortholog: mtu1874 (OG4_10600); Phenotype: non-essential; Source study: nmpdr Gene/Ortholog: mtu1142 (OG4_10600); Phenotype: essential; Source study: nmpdr Gene/Ortholog: eco1968 (OG4_10600); Phenotype: undefined; Source study: blattner Gene/Ortholog: eco1968 (OG4_10600); Phenotype: non-essential; Source study: gerdes Gene/Ortholog: eco1968 (OG4_10600); Phenotype: non-essential; Source study: keio Gene/Ortholog: eco1968 (OG4_10600); Phenotype: non-essential; Source study: shigen Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Larval/Adult Lethal/Arrest; Source study: neb Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Embryonic Lethal/Arrest; Source study: neb Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Embryonic Lethal/Arrest; Source study: wormbase Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Larval/Adult Lethal/Arrest; Source study: wormbase Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in bloodstream forms (3 days); Source study: alsford Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in procyclic forms; Source study: alsford Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in differentiation of procyclic to bloodstream forms; Source study: alsford Is it a monomer or multimer as biological unit? (make prediction athttp://www.ebi.ac.uk/msd-srv/prot_int/pistart.html): Complex of proteins?: Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism): Druggability index (range: 0 to 1): 0.6 http://www.sciencedirect.com/science/article/pii/S0968089608001260 http://pubs.acs.org/doi/abs/10.1021/jm031066i
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure (PDB or Homology model) -- PDB # or closest PDB entry if using homology model: 2IYO -- For Homology Model option: ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
Chain A, Structural Characterization Of A Bacterial 6pdh Reveals Aspects Of Specificity, Mechanism And Mode Of InhibitionSequence ID: 2IYO_ALength: 472Number of Matches: 1
Alignment statistics for match #1 Score
Expect
Method
Identities
Positives
Gaps
390 bits(1003)
1e-131
Compositional matrix adjust.
207/502(41%)
301/502(59%)
37/502(7%)
<span style="font-size: 11.869px;">Query 3 CDVGIYGLAVMGLGLSLNLASRGIRVSVCNRTSTKVDGALKQAKDENFEENIFGARTLED 62
+ G+ G+AVMG L+LN+ SRG V++ NRT++K + K+ +D+N +F +TLE+
Sbjct 4 ANFGVVGMAVMGKNLALNVESRGYTVAIYNRTTSKTEEVFKEHQDKNL---VF-TKTLEE 59
Query 63 FVQSLKKPRRIIMVIEAGAPVDALINHLLPKLDAGDCLVDAGNEFFEVSEKRERLCASKG 122
FV SL+KPRRI+++++AGA DA I LLP LD GD L+D GN F + +R A G
Sbjct 60 FVGSLEKPRRIMLMVQAGAATDATIKSLLPLLDIGDILIDGGNTHFPDTMRRNAELADSG 119
Query 123 VLFMDVGLCAGEGGARSGPPLTPGGSLEAWNLMEPIFVQLAGKIDASKTIPLPGALTVSD 182
+ F+ G+ GE GA GP + PGG EA++L+ PIF Q+A K P G
Sbjct 120 INFIGTGVSGGEKGALLGPSMMPGGQKEAYDLVAPIFEQIAAKA------PQDG------ 167
Query 183 EEKQNACVSHLGPCGAGHYVKMVHNGIMYGDMQLIAEAHQLLKFACDLSNEELHVTFKKW 242
CV+++G GAGHYVKMVHNGI YGDMQLIAE++ LLK LSN E+ F++W
Sbjct 168 ----KPCVAYMGANGAGHYVKMVHNGIEYGDMQLIAESYDLLKRILGLSNAEIQAIFEEW 223
Query 243 NEDELHSYLLGITANIVRKKDSFTGGYLLDFIADTAGSKGTGKWTMQQAAELGVAVPTIT 302
NE EL SYL+ IT ++++KD GY++D I D AG+KGTGKWT + A +LGV +P IT
Sbjct 224 NEGELDSYLIEITKEVLKRKDDEGEGYIVDKILDKAGNKGTGKWTSESALDLGVPLPLIT 283
Query 303 AALDMRYICSNQPLRQKMNCLYAQNWCSLVKTEDSTKEQRIESIRRALVCGRICCFAQGM 362
++ RYI + + R K + + + K++ IE IR+AL +I +AQG
Sbjct 284 ESVFARYISTYKDERVKASKVLSGPALDF----SGDKKEVIEKIRKALYFSKIMSYAQGF 339
Query 363 HLLRVISEQKGWGVDLSEVSRIWQAGCVIECDFLKVMQRAFRKKPDLESILLSEEVHTTV 422
LR SE+ W + +++IW+AGC+I +FL+ + AF K +LE++LL +
Sbjct 340 AQLRKASEEFDWDLPYGTIAQIWRAGCIIRAEFLQNITDAFDKDSELENLLLDDYFVDIT 399
Query 423 QNYLPALQEVISLSLGTATPRPDEPSVRITLPTPAHSASYNYLASSCGLRLSMNLVQAQR 482
+ Y A+++V+SL++ T P P +++ +Y S L NL+QAQR
Sbjct 400 KRYQEAVRDVVSLAVQAGT------------PIPTFTSAISYYDSYRSENLPANLIQAQR 447
Query 483 DCFGAHHFKRTDREGKYHVEDW 504
D FGAH ++RTD+ G +H DW
Sbjct 448 DYFGAHTYERTDKAGIFHY-DW 468</span>
---- Query Coverage: 99% ---- Max % Identities: 41% ---- % Positives: 59% ---- Chain used for homology: Chain A
Figure 1: PDB structure for Chain A, Structural Characterization Of A Bacterial 6-phosphogluconate dehydrogenase Reveals Aspects Of Specificity, Mechanism And Mode Of Inhibition
Current Inhibitors: There are currently 381 inhibitors of this target. Expression Information (has it been expressed in bacterial cells): Has not been expressed in bacterial cells. Purification Method: Since it hasn't been expressed, there is no purification method for this target. Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MSCDVGIYGLAVMGLGLSLNLASRGIRVSVCNRTSTKVDGALKQAKDENFEENIFGARTLEDFVQSLKKPRRIIMVIEAG
APVDALINHLLPKLDAGDCLVDAGNEFFEVSEKRERLCASKGVLFMDVGLCAGEGGARSGPPLTPGGSLEAWNLMEPIFV
QLAGKIDASKTIPLPGALTVSDEEKQNACVSHLGPCGAGHYVKMVHNGIMYGDMQLIAEAHQLLKFACDLSNEELHVTFK
KWNEDELHSYLLGITANIVRKKDSFTGGYLLDFIADTAGSKGTGKWTMQQAAELGVAVPTITAALDMRYICSNQPLRQKM
NCLYAQNWCSLVKTEDSTKEQRIESIRRALVCGRICCFAQGMHLLRVISEQKGWGVDLSEVSRIWQAGCVIECDFLKVMQ
RAFRKKPDLESILLSEEVHTTVQNYLPALQEVISLSLGTATPRPDEPSVRITLPTPAHSASYNYLASSCGLRLSMNLVQA
QRDCFGAHHFKRTDREGKYHVEDWGA
*length of your protein in Amino Acids: 506 Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 55586.93 Molar Extinction coefficient of your protein at 280 nm wavelength: 56015 TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
results
*CDS Gene Sequence (paste as text only):
*GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol) -- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
*NCBI Gene # or RefSeq#:
*Protein ID (NP or XP #) or Wolbachia#: TGME49_242600-t26_1
*Organism (including strain): Toxoplasma gondii
Etiologic Risk Group (see link below):
*/Disease Information (sort of like the Intro to your Mini Research Write up): Toxoplasma gondii is a single-celled parasite that causes the disease known as toxoplasmosis. In the United States alone, more than 60 million people are infected with the parasite, however very few express symptoms because a healthy person's immune system usually keeps the parasite from causing illness. Pregnant women and individuals with compromised immune systems are the most at risk for contracting taxoplasmosis. The most common way of getting a taxoplasma infection is through the consumption or handling (and not washing hands properly) of undercooked meat.
Link to TDR Targets page (if present): http://www.tdrtargets.org/targets/view?gene_id=258054
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.): http://toxodb.org/toxo/app/record/gene/TGME49_042600
Essentiality of this protein:
TGME49_042600 has essentiality data
Gene/Ortholog: mtu1874 (OG4_10600); Phenotype: non-essential; Source study: nmpdr
Gene/Ortholog: mtu1142 (OG4_10600); Phenotype: essential; Source study: nmpdr
Gene/Ortholog: eco1968 (OG4_10600); Phenotype: undefined; Source study: blattner
Gene/Ortholog: eco1968 (OG4_10600); Phenotype: non-essential; Source study: gerdes
Gene/Ortholog: eco1968 (OG4_10600); Phenotype: non-essential; Source study: keio
Gene/Ortholog: eco1968 (OG4_10600); Phenotype: non-essential; Source study: shigen
Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Larval/Adult Lethal/Arrest; Source study: neb
Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Embryonic Lethal/Arrest; Source study: neb
Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Embryonic Lethal/Arrest; Source study: wormbase
Gene/Ortholog: cel16317 (OG4_10600); Phenotype: Larval/Adult Lethal/Arrest; Source study: wormbase
Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in bloodstream forms (3 days); Source study: alsford
Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in bloodstream forms (6 days); Source study: alsford
Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in procyclic forms; Source study: alsford
Gene/Ortholog: Tb09.211.3180 (OG4_10600); Phenotype: significant loss of fitness in differentiation of procyclic to bloodstream forms; Source study: alsford
Is it a monomer or multimer as biological unit? (make prediction at http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html):
Complex of proteins?:
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
Druggability index (range: 0 to 1): 0.6
http://www.sciencedirect.com/science/article/pii/S0968089608001260
http://pubs.acs.org/doi/abs/10.1021/jm031066i
*EC#: 1.1.1.44
Link to BRENDA EC# page: http://www.brenda-enzymes.org/enzyme.php?ecno=1.1.1.44
-- Show screenshot of BRENDA enzyme mechanism schematic
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
Method: Continuous Spectrophotometric Rate Determination
http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Enzyme_Assay/6phosphoglucdehydrog75.pdf
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 2IYO
-- For Homology Model option:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
Chain A, Structural Characterization Of A Bacterial 6pdh Reveals Aspects Of Specificity, Mechanism And Mode Of InhibitionSequence ID: 2IYO_ALength: 472Number of Matches: 1
Alignment statistics for match #1
Score
<span style="font-size: 11.869px;">Query 3 CDVGIYGLAVMGLGLSLNLASRGIRVSVCNRTSTKVDGALKQAKDENFEENIFGARTLED 62 + G+ G+AVMG L+LN+ SRG V++ NRT++K + K+ +D+N +F +TLE+ Sbjct 4 ANFGVVGMAVMGKNLALNVESRGYTVAIYNRTTSKTEEVFKEHQDKNL---VF-TKTLEE 59 Query 63 FVQSLKKPRRIIMVIEAGAPVDALINHLLPKLDAGDCLVDAGNEFFEVSEKRERLCASKG 122 FV SL+KPRRI+++++AGA DA I LLP LD GD L+D GN F + +R A G Sbjct 60 FVGSLEKPRRIMLMVQAGAATDATIKSLLPLLDIGDILIDGGNTHFPDTMRRNAELADSG 119 Query 123 VLFMDVGLCAGEGGARSGPPLTPGGSLEAWNLMEPIFVQLAGKIDASKTIPLPGALTVSD 182 + F+ G+ GE GA GP + PGG EA++L+ PIF Q+A K P G Sbjct 120 INFIGTGVSGGEKGALLGPSMMPGGQKEAYDLVAPIFEQIAAKA------PQDG------ 167 Query 183 EEKQNACVSHLGPCGAGHYVKMVHNGIMYGDMQLIAEAHQLLKFACDLSNEELHVTFKKW 242 CV+++G GAGHYVKMVHNGI YGDMQLIAE++ LLK LSN E+ F++W Sbjct 168 ----KPCVAYMGANGAGHYVKMVHNGIEYGDMQLIAESYDLLKRILGLSNAEIQAIFEEW 223 Query 243 NEDELHSYLLGITANIVRKKDSFTGGYLLDFIADTAGSKGTGKWTMQQAAELGVAVPTIT 302 NE EL SYL+ IT ++++KD GY++D I D AG+KGTGKWT + A +LGV +P IT Sbjct 224 NEGELDSYLIEITKEVLKRKDDEGEGYIVDKILDKAGNKGTGKWTSESALDLGVPLPLIT 283 Query 303 AALDMRYICSNQPLRQKMNCLYAQNWCSLVKTEDSTKEQRIESIRRALVCGRICCFAQGM 362 ++ RYI + + R K + + + K++ IE IR+AL +I +AQG Sbjct 284 ESVFARYISTYKDERVKASKVLSGPALDF----SGDKKEVIEKIRKALYFSKIMSYAQGF 339 Query 363 HLLRVISEQKGWGVDLSEVSRIWQAGCVIECDFLKVMQRAFRKKPDLESILLSEEVHTTV 422 LR SE+ W + +++IW+AGC+I +FL+ + AF K +LE++LL + Sbjct 340 AQLRKASEEFDWDLPYGTIAQIWRAGCIIRAEFLQNITDAFDKDSELENLLLDDYFVDIT 399 Query 423 QNYLPALQEVISLSLGTATPRPDEPSVRITLPTPAHSASYNYLASSCGLRLSMNLVQAQR 482 + Y A+++V+SL++ T P P +++ +Y S L NL+QAQR Sbjct 400 KRYQEAVRDVVSLAVQAGT------------PIPTFTSAISYYDSYRSENLPANLIQAQR 447 Query 483 DCFGAHHFKRTDREGKYHVEDW 504 D FGAH ++RTD+ G +H DW Sbjct 448 DYFGAHTYERTDKAGIFHY-DW 468</span>---- Query Coverage: 99%
---- Max % Identities: 41%
---- % Positives: 59%
---- Chain used for homology: Chain A
Current Inhibitors: There are currently 381 inhibitors of this target.
Expression Information (has it been expressed in bacterial cells): Has not been expressed in bacterial cells.
Purification Method: Since it hasn't been expressed, there is no purification method for this target.
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
MSCDVGIYGLAVMGLGLSLNLASRGIRVSVCNRTSTKVDGALKQAKDENFEENIFGARTLEDFVQSLKKPRRIIMVIEAG
APVDALINHLLPKLDAGDCLVDAGNEFFEVSEKRERLCASKGVLFMDVGLCAGEGGARSGPPLTPGGSLEAWNLMEPIFV
QLAGKIDASKTIPLPGALTVSDEEKQNACVSHLGPCGAGHYVKMVHNGIMYGDMQLIAEAHQLLKFACDLSNEELHVTFK
KWNEDELHSYLLGITANIVRKKDSFTGGYLLDFIADTAGSKGTGKWTMQQAAELGVAVPTITAALDMRYICSNQPLRQKM
NCLYAQNWCSLVKTEDSTKEQRIESIRRALVCGRICCFAQGMHLLRVISEQKGWGVDLSEVSRIWQAGCVIECDFLKVMQ
RAFRKKPDLESILLSEEVHTTVQNYLPALQEVISLSLGTATPRPDEPSVRITLPTPAHSASYNYLASSCGLRLSMNLVQA
QRDCFGAHHFKRTDREGKYHVEDWGA
*length of your protein in Amino Acids: 506
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 55586.93
Molar Extinction coefficient of your protein at 280 nm wavelength: 56015
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):